How do I export multiple separate objects in an obj file?
The lines that follow show that your two cubes are contained as two separate objects:
*snip*
o Cube.001
*snip*
o Cube
*snip*

If the point of failure is how they behave upon import into Unity, it may be better to phrase the question for that community.
Also, exports to FBX are supported in Blender: http://docs.unity3d.com/Manual/HOWTO-ImportObjectBlender.html
In any case, there's no way to further separate the object coordinates in obj format than they are already, other than exporting each cube to it's own file.
Are you perhaps asking &quot;How do I independently manipulate two objects from a single obj file in Unity?&quot;?
Hope that helps.